If you were a dog just over 100 years ago, life would have been simple. You would likely have been gainfully employed – perhaps hunting, herding or guarding – and provided you did your job, your owners would have accepted that you were sometimes messy, loud or unpredictable. Most dogs today are never expected to work, even though they are often still tuned into functions their breed has fulfilled for thousands of years. Instead, they are expected to behave like small children, yet be as independent as adults. To make things worse, our culture is awash with myths that prevent dogs being properly understood – in particular, the enduring idea that they harbour a powerful desire to dominate their family pack. Put simply: dogs are on the brink of a crisis. And as we have put them there, it is our responsibility to help them.

This is the thesis of John Bradshaw's scholarly yet passionate book In Defence of Dogs, which is nothing less than a manifesto for a new understanding of our canine friends. It is an attempt to "stand up for dogdom" – that is, dogs as they truly are, not as we assume they are. As a canine expert and dog-lover, Bradshaw is dismayed that our treatment of dogs is based on so many mistaken beliefs and assumptions. He wants to set the record straight now because canine science has made huge advances in recent decades.

He starts by demolishing the notion that dogs are essentially aggressive creatures seeking dominance, which is based on discredited research into wolf packs. It is now known that wolves – the direct ancestors of dogs – actually live in harmonious family groups. Packs are not dominated by "alpha wolves", but are fundamentally cooperative. Bradshaw is determined that the "dominance theory" be banished. But while enlightened trainers and owners have got the message, many more still subscribe to techniques aimed at ingraining fear and subservience into dogs. For Bradshaw, these are not only misguided and cruel, but joyless.

His account of the evolution of dogs is fascinating. Surveying the latest research, he concludes that the dog's epic journey towards domestication probably started around 20,000 years ago. Dogs have become almost a separate species from wolves, and their evolution continues to confound biologists. What Bradshaw is keen to stress, though, is the unique evolutionary pact between humans and dogs: we have programmed into them a deep need for relationships with humans, which we must treat with respect.

This material underpins Bradshaw's most compelling chapters, which explore the emotional lives of dogs. The revelation here for many dog owners might perhaps be that dogs' emotional repertoires are much more limited than we generally think. Research confirms that most dog owners are convinced their dogs can feel and display complex emotions – particularly guilt. In fact, there is almost no evidence for this; dogs simply do not have the self-awareness for such emotions. But in persisting with the notion that dogs have this advanced understanding of their actions – and our expectations – we end up punishing them in ways they cannot understand. Dogs are specialists in love, fear and joy. But we must stop assuming their knowledge of emotions beyond their grasp.

Elsewhere in these sections, Bradshaw tackles the question: "Does your dog love you?" The answer is yes: probably even more than you think. Dogs are profoundly attached to their owners, and this love – a term Bradshaw happily uses – is often at the root of their apparent misbehaviour. For example, dogs not properly trained to understand that when we leave we will return can be plunged into the depths of anxiety when we are not around. Bradshaw estimates that up to 20% of dogs suffer from "separation distress" when left alone at home.

Most people can probably intuit that human progress has cut many dogs off from the activities that previously gave their lives meaning. (Anyone who has spent time with a border collie will know that their boundless desire to herd everything from pushchairs to small children betokens something of a behavioural hangover.) And Bradshaw's arguments against pedigree breeding play into an existing public debate (breeds heading for extinction due to the demand for perfection).

His sober argument finds an unlikely echo in Jan Bondeson's slightly bewildering volume Amazing Dogs (Amberley Publishing, £20). An eccentric romp through canine history, it nevertheless shares the same thesis: dogs are poorly served by our misunderstanding of them. This is made clear in his chapters on the glum history of "canine intellectuals", who wowed 19th-century crowds around Europe with their supposed skills – from poetry to arithmetic to clairvoyance. Elsewhere he celebrates the true over-achievers from canine history: Shakespearean actors, charity-collectors, and dogs whose loyalty resulted in years-long graveside vigils for their dead masters.